Molecular Characterization and Cross-Reactivity of Feline Calicivirus Circulating in Southwestern China

Feline calicivirus (FCV) is an important pathogen of cats that has two genogroups (GI and GII). To investigate the prevalence and molecular characteristics of FCVs in southwestern China, 162 nasal swab samples were collected from cats in animal shelters and pet hospitals. In total, 38 of the clinical samples (23.46%) were identified as FCV positive using nested RT-PCR. Phylogenetic analyses using 10 capsid protein VP1 sequences revealed that 8 GI and 2 GII strains formed two independent clusters. Additionally, three separated FCVs that were not clustered phylogenetically (two GI and one GII strains) were successfully isolated from clinical samples and their full-length genomes were obtained. Phylogenetic and recombinant analyses of a GI FCV revealed genomic breakpoints in ORF1 and ORF2 regions with evidence for recombinant events between GI sub-genogroups, which is reported in China for the first time. Furthermore, sera obtained from mice immunized independently with the three FCV isolates and a commercial vaccine were used to evaluate the cross-reactivity of neutralizing antibodies. The three separate FCVs were neutralized by each other at a 1:19 to 1:775 titer range, whereas the triple-inactivated vaccine was at a titer of 1:16, which suggested that different genogroup/sub-genogroup FCV strains exhibit significantly different titers of neutralizing antibodies, including the commercial FCV vaccine. Thus, our study revealed the genetic diversity and complex cross-reactivity levels of FCVs in southwestern China, which provides new insights for application in vaccination strategies.

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Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020

Viruses ◽

10.3390/v12080877 ◽

2020 ◽

Vol 12 (8) ◽

pp. 877 ◽

Cited By ~ 1

Author(s):

Jun Hayakawa ◽

Tomomi Masuko ◽

Tae Takehana ◽

Tohru Suzuki

Keyword(s):

Cell Culture ◽

Respiratory Diseases ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Cross Reactivity ◽

Molecular Characteristics ◽

Bovine Respiratory Diseases ◽

Antigenic Characterization ◽

New Genotype

Influenza D virus (IDV), which is a new member of the Orthomyxoviridae family, is potentially involved in bovine respiratory diseases (BRDs). Bovine IDVs (BIDVs) from Japan have been distributed nationwide since 2010 and are genetically distinct from foreign IDVs. We isolated BIDVs from three BRD outbreaks, in Hokkaido during 2018–2020, to understand their genetic and antigenic characteristics. Retrospective surveillance was performed using sera collected throughout the last decade in Hokkaido to investigate BIDV existence. Three BIDVs were isolated using cell culture. Comparative and phylogenetic analyses using sequence data of the three BIDVs and IDVs from Japan and other countries available in GenBank demonstrated that Japanese BIDVs, including the three BIDV isolates, were genetically distinct from other IDVs. Genotype classifications based on the rotavirus genotype classification revealed multiple genotypes of RNA segments 1–7. Two BIDVs were of a new genotype, different from those of other Japanese BIDVs. Neutralization assays against two BIDVs with different genotypes using sera collected in acute and recovery phases of BRD revealed differences in cross-reactivity to heterogenous BIDVs. Retrospective surveillance suggested that BIDV existed in Hokkaido, in 2009. Our findings suggest that BIDVs of different genotypes and antigenicity are distributed and maintained in Hokkaido and provide new insights into molecular characteristics and the evolution of IDVs.

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Antigenic and Cryo-Electron Microscopy Structure Analysis of a Chimeric Sapovirus Capsid

Journal of Virology ◽

10.1128/jvi.02916-15 ◽

2015 ◽

Vol 90 (5) ◽

pp. 2664-2675 ◽

Cited By ~ 7

Author(s):

Naoyuki Miyazaki ◽

David W. Taylor ◽

Grant S. Hansman ◽

Kazuyoshi Murata

Keyword(s):

Electron Microscopy ◽

Insect Cells ◽

Homology Model ◽

Cross Reactivity ◽

Chimeric Vlps ◽

Cryo Electron Microscopy ◽

P Domain ◽

Capsid Protein Vp1 ◽

First Time ◽

Icosahedral Particle

ABSTRACTThe capsid protein (VP1) of all caliciviruses forms an icosahedral particle with two principal domains, shell (S) and protruding (P) domains, which are connected via a flexible hinge region. The S domain forms a scaffold surrounding the nucleic acid, while the P domains form a homodimer that interacts with receptors. The P domain is further subdivided into two subdomains, termed P1 and P2. The P2 subdomain is likely an insertion in the P1 subdomain; consequently, the P domain is divided into the P1-1, P2, and P1-2 subdomains. In order to investigate capsid antigenicity, N-terminal (N-term)/S/P1-1 and P2/P1-2 were switched between two sapovirus genotypes GI.1 and GI.5. The chimeric VP1 constructs were expressed in insect cells and were shown to self-assemble into virus-like particles (VLPs) morphologically similar to the parental VLPs. Interestingly, the chimeric VLPs had higher levels of cross-reactivities to heterogeneous antisera than the parental VLPs. In order to better understand the antigenicity from a structural perspective, we determined an intermediate-resolution (8.5-Å) cryo-electron microscopy (cryo-EM) structure of a chimeric VLP and developed a VP1 homology model. The cryo-EM structure revealed that the P domain dimers were raised slightly (∼5 Å) above the S domain. The VP1 homology model allowed us predict the S domain (67–229) and P1-1 (229–280), P2 (281–447), and P1-2 (448–567) subdomains. Our results suggested that the raised P dimers might expose immunoreactive S/P1-1 subdomain epitopes. Consequently, the higher levels of cross-reactivities with the chimeric VLPs resulted from a combination of GI.1 and GI.5 epitopes.IMPORTANCEWe developed sapovirus chimeric VP1 constructs and produced the chimeric VLPs in insect cells. We found that both chimeric VLPs had a higher level of cross-reactivity against heterogeneous VLP antisera than the parental VLPs. The cryo-EM structure of one chimeric VLP (Yokote/Mc114) was solved to 8.5-Å resolution. A homology model of the VP1 indicated for the first time the putative S and P (P1-1, P2, and P1-2) domains. The overall structure of Yokote/Mc114 contained features common among other caliciviruses. We showed that the P2 subdomain was mainly involved in the homodimeric interface, whereas a large gap between the P1 subdomains had fewer interactions.

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Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

Journal of Fungi ◽

10.3390/jof7060478 ◽

2021 ◽

Vol 7 (6) ◽

pp. 478

Author(s):

Xue-Wei Wang ◽

Tom W. May ◽

Shi-Liang Liu ◽

Li-Wei Zhou

Keyword(s):

Phylogenetic Analyses ◽

Taxonomic Status ◽

Ancestral State ◽

Trait Evolution ◽

Natural Classification ◽

Multiple Loci ◽

The Family ◽

Phylogenetic Perspective ◽

Taxonomic Framework ◽

First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

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Aptamer BC 007’s Affinity to Specific and Less-Specific Anti-SARS-CoV-2 Neutralizing Antibodies

Viruses ◽

10.3390/v13050932 ◽

2021 ◽

Vol 13 (5) ◽

pp. 932

Author(s):

Annekathrin Haberland ◽

Oxana Krylova ◽

Heike Nikolenko ◽

Peter Göttel ◽

Andre Dallmann ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Cross Reactivity ◽

Enzyme Linked Immunosorbent Assay ◽

Resonance Spectroscopy ◽

Plastic Plate ◽

Calorimetric Titration ◽

Background Signal ◽

High Background ◽

Specific Virus ◽

Binding Sequence

COVID-19 is a pandemic respiratory disease that is caused by the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Anti-SARS-CoV-2 antibodies are essential weapons that a patient with COVID-19 has to combat the disease. When now repurposing a drug, namely an aptamer that interacts with SARS-CoV-2 proteins for COVID-19 treatment (BC 007), which is, however, a neutralizer of pathogenic autoantibodies in its original indication, the possibility of also binding and neutralizing anti-SARS-CoV-2 antibodies must be considered. Here, the highly specific virus-neutralizing antibodies have to be distinguished from the ones that also show cross-reactivity to tissues. The last-mentioned could be the origin of the widely reported SARS-CoV-2-induced autoimmunity, which should also become a target of therapy. We, therefore, used enzyme-linked immunosorbent assay (ELISA) technology to assess the binding of well-characterized publicly accessible anti-SARS-CoV-2 antibodies (CV07-209 and CV07-270) with BC 007. Nuclear magnetic resonance spectroscopy, isothermal calorimetric titration, and circular dichroism spectroscopy were additionally used to test the binding of BC 007 to DNA-binding sequence segments of these antibodies. BC 007 did not bind to the highly specific neutralizing anti-SARS-CoV-2 antibody but did bind to the less specific one. This, however, was a lot less compared to an autoantibody of its original indication (14.2%, range 11.0–21.5%). It was also interesting to see that the less-specific anti-SARS-CoV-2 antibody also showed a high background signal in the ELISA (binding on NeutrAvidin-coated or activated but noncoated plastic plate). These initial experiments suggest that the risk of binding and neutralizing highly specific anti-SARS CoV-2 antibodies by BC 007 should be low.

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Two New Haplotypes of Bartonella sp. Isolated from Lipoptena fortisetosa (Diptera: Hippoboscidae) in SE Poland

Insects ◽

10.3390/insects12060485 ◽

2021 ◽

Vol 12 (6) ◽

pp. 485

Author(s):

Katarzyna Bartosik ◽

Weronika Maślanko ◽

Alicja Buczek ◽

Marek Asman ◽

Joanna Witecka ◽

...

Keyword(s):

Potential Role ◽

Roe Deer ◽

Phylogenetic Analyses ◽

Rpob Gene ◽

Molecular Characteristics ◽

Broad Host Range ◽

South Eastern ◽

Se Poland ◽

Pcr Method ◽

The Subject

Insects of the genus Lipoptena are parasitic arthropods with a broad host range. Due to the type of parasitism (hematophagy), their potential role as vectors of pathogens, i.e., Bartonella sp., Anaplasma phagocytophilum, Rickettsia spp., and Borrelia burgdorferi is considered. As the range of their occurrence has been changing dynamically in recent years and infestations of humans have increasingly been reported, these organisms are now the subject of numerous studies. Our research aimed to present the molecular characteristics of Bartonella sp. detected in Lipoptena fortisetosa parasitizing wild cervids in south-eastern Poland. Adults of Lipoptena spp. were collected from carcasses of roe deer and red deer between spring and autumn in 2013. The PCR method was used to detect Bartonella sp. in the insects. We report two new haplotypes of the rpoB gene of Bartonella sp. isolated from L. fortisetosa feeding on wild cervids in south-eastern Poland and the presence of this invasive ectoparasitic species in the studied area since 2013. Phylogenetic analyses of newly obtained Bartonella sp. haplotypes confirmed their unique position on the constructed tree and network topology. The rpoB gene sequences found belonging to lineage B support the view that this phylogenetic lineage represents a novel Bartonella species.

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Evaluation of mobile real-time polymerase chain reaction tests for the detection of severe acute respiratory syndrome coronavirus 2

Scientific Reports ◽

10.1038/s41598-021-88625-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Chukwunonso Onyilagha ◽

Henna Mistry ◽

Peter Marszal ◽

Mathieu Pinette ◽

Darwyn Kobasa ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Real Time ◽

Point Of Care ◽

Middle Eastern ◽

Turnaround Time ◽

Cross Reactivity ◽

Clinical Samples ◽

Diarrhea Virus ◽

Highly Sensitive ◽

Transmissible Gastroenteritis

AbstractThe coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), calls for prompt and accurate diagnosis and rapid turnaround time for test results to limit transmission. Here, we evaluated two independent molecular assays, the Biomeme SARS-CoV-2 test, and the Precision Biomonitoring TripleLock SARS-CoV-2 test on a field-deployable point-of-care real-time PCR instrument, Franklin three9, in combination with Biomeme M1 Sample Prep Cartridge Kit for RNA 2.0 (M1) manual extraction system for rapid, specific, and sensitive detection of SARS-COV-2 in cell culture, human, and animal clinical samples. The Biomeme SARS-CoV-2 assay, which simultaneously detects two viral targets, the orf1ab and S genes, and the Precision Biomonitoring TripleLock SARS-CoV-2 assay that targets the 5′ untranslated region (5′ UTR) and the envelope (E) gene of SARS-CoV-2 were highly sensitive and detected as low as 15 SARS-CoV-2 genome copies per reaction. In addition, the two assays were specific and showed no cross-reactivity with Middle Eastern respiratory syndrome coronavirus (MERS-CoV), infectious bronchitis virus (IBV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis (TGE) virus, and other common human respiratory viruses and bacterial pathogens. Also, both assays were highly reproducible across different operators and instruments. When used to test animal samples, both assays equally detected SARS-CoV-2 genetic materials in the swabs from SARS-CoV-2-infected hamsters. The M1 lysis buffer completely inactivated SARS-CoV-2 within 10 min at room temperature enabling safe handling of clinical samples. Collectively, these results show that the Biomeme and Precision Biomonitoring TripleLock SARS-CoV-2 mobile testing platforms could reliably and promptly detect SARS-CoV-2 in both human and animal clinical samples in approximately an hour and can be used in remote areas or health care settings not traditionally serviced by a microbiology laboratory.

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Immune Evasion of SARS-CoV-2 Variants of Concern is Driven by Low Affinity to Neutralizing Antibodies

Chemical Communications ◽

10.1039/d1cc01747k ◽

2021 ◽

Author(s):

Matheus Ferraz ◽

Emerson Moreira ◽

Danilo F. Coêlho ◽

Gabriel Wallau ◽

Roberto Lins

Keyword(s):

Immune Evasion ◽

Neutralizing Antibodies ◽

Cross Reactivity ◽

Class I ◽

Minor Role ◽

A Minor

SARS-CoV-2 VOCs immune evasion is mainly due to lower cross-reactivity from previously elicited class I/II neutralizaing antibodies, while increased affinity to hACE2 plays a minor role. Affinity between antibodies and...

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Infundibulicybe rufa sp. nov. (Tricholomataceae), a reddish brown species from southwestern China

Phytotaxa ◽

10.11646/phytotaxa.266.2.7 ◽

2016 ◽

Vol 266 (2) ◽

pp. 134 ◽

Cited By ~ 2

Author(s):

QI ZHAO ◽

YAN-JIA HAO ◽

JIAN-KUI LIU ◽

KEVIN D. HYDE ◽

YANG-YANG CUI ◽

...

Keyword(s):

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Biosphere Reserve ◽

Its Region ◽

Southwestern China ◽

New Taxon ◽

Line Drawings ◽

Phylogenetic Placement ◽

Molecular Phylogenetic ◽

Pileus Surface

Infundibulicybe rufa sp. nov., is described from Jiuzhaigou Biosphere Reserve, southwestern China. It is characterized by the combination of the following characters: umbilicate to slightly infundibuliform, reddish brown pileus; decurrent, cream lamellae; cylindrical stipe concolorous with the pileus surface. Molecular phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) region indicates that I. rufa is closely related to I. mediterranea and I. bresadolana. A description, line drawings, phylogenetic placement and comparison with allied taxa for the new taxon are presented.

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Biological and Molecular Characteristics of a Novel Partitivirus Infecting the Edible Fungus Lentinula edodes

Plant Disease ◽

10.1094/pdis-07-16-0951-re ◽

2017 ◽

Vol 101 (5) ◽

pp. 726-733 ◽

Cited By ~ 15

Author(s):

Mengpei Guo ◽

Yinbing Bian ◽

Jinjie Wang ◽

Gangzheng Wang ◽

Xiaolong Ma ◽

...

Keyword(s):

Lentinula Edodes ◽

Control Strategies ◽

Phylogenetic Analyses ◽

Pcr Analysis ◽

Molecular Characteristics ◽

Rt Pcr ◽

Edible Fungus ◽

Qpcr Analysis ◽

Disease Diagnostics ◽

Wild Strains

A new partitivirus named Lentinula edodes partitivirus 1 (LePV1) was isolated from a diseased L. edodes strain with severe degeneration of the mycelium and imperfect browning in bag cultures. The nucleotide sequences of LePV1 dsRNA-1 and dsRNA-2 were determined; they were 2,382 bp and 2,245 bp in length, and each contained a single ORF encoding RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. The purified virus preparation contained isometric particles 34 nm in diameter encapsidating these dsRNAs. Phylogenetic analyses showed LePV1 to be a new member of Betapartitivirus, with the RdRp sequence most closely related to Grapevine partitivirus. RT-PCR analysis showed that 27 of the 56 Chinese L. edodes core collection strains carry LePV1, with the virus being more common in wild strains than cultivated strains. In addition, qPCR analysis suggested that coinfection with L. edodes mycovirus HKB (LeV-HKB) could increase replication of the RdRp gene of LePV1. This study may be essential for the development of more accurate disease diagnostics and the formulation of control strategies for viral diseases in L. edodes.

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Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510199112 ◽

2015 ◽

Vol 112 (33) ◽

pp. 10473-10478 ◽

Cited By ~ 128

Author(s):

Davide Corti ◽

Jincun Zhao ◽

Mattia Pedotti ◽

Luca Simonelli ◽

Sudhakar Agnihothram ◽

...

Keyword(s):

B Cells ◽

Neutralizing Antibodies ◽

Human Monoclonal Antibody ◽

Infected Individual ◽

Chinese Hamster ◽

Neutralizing Antibody ◽

Emerging Viruses ◽

Antiviral Therapies ◽

Human Infections ◽

First Time

Middle East Respiratory Syndrome (MERS) is a highly lethal pulmonary infection caused by a previously unidentified coronavirus (CoV), likely transmitted to humans by infected camels. There is no licensed vaccine or antiviral for MERS, therefore new prophylactic and therapeutic strategies to combat human infections are needed. In this study, we describe, for the first time, to our knowledge, the isolation of a potent MERS-CoV–neutralizing antibody from memory B cells of an infected individual. The antibody, named LCA60, binds to a novel site on the spike protein and potently neutralizes infection of multiple MERS-CoV isolates by interfering with the binding to the cellular receptor CD26. Importantly, using mice transduced with adenovirus expressing human CD26 and infected with MERS-CoV, we show that LCA60 can effectively protect in both prophylactic and postexposure settings. This antibody can be used for prophylaxis, for postexposure prophylaxis of individuals at risk, or for the treatment of human cases of MERS-CoV infection. The fact that it took only 4 mo from the initial screening of B cells derived from a convalescent patient for the development of a stable chinese hamster ovary (CHO) cell line producing neutralizing antibodies at more than 5 g/L provides an example of a rapid pathway toward the generation of effective antiviral therapies against emerging viruses.

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